Merge pull request #26 from mzmine/library-handler

Implemented return metadata in return user validation info

library_spectra_validation/library_handler.py

@@ -1,7 +1,8 @@
 from matchms.importing import load_spectra
 from matchms.filtering.SpectrumProcessor import SpectrumProcessor
 from filters import PRIMARY_FILTERS
-from validation_pipeline import Modification, SpectrumRepairer, SpectrumValidator
+from validation_pipeline import METADATA_FIELDS_OF_INTEREST, Modification, SpectrumRepairer, SpectrumValidator
+import pandas as pd
 
 class LibraryHandler:
     """Stores the 3 different types of spectra. Correct, repaired, wrong.
@@ -69,8 +70,10 @@ def return_user_validation_info(self, spectrum_id):
 
         modifications = self.modifications[spectrum_id]
         failed_requirements = self.failed_requirements[spectrum_id]
-
-        return modifications, failed_requirements, self.spectra[spectrum_id]
+        metadata = pd.DataFrame(self.spectra[spectrum_id].metadata, index=["Value"])
+        metadata = metadata.T
+        metadata = metadata.loc[metadata.index.isin(METADATA_FIELDS_OF_INTEREST)]
+        return modifications, failed_requirements, metadata
 
     def approve_repair(self, spectrum_id, field_name):
         """Accepts every modification done to a field_name"""
@@ -157,7 +160,5 @@ def user_rerun_repair(self, spectrum_id, rerun: bool):
         if rerun: #todo do we even need it??
             self.modifications[spectrum_id] = self.spectrum_repairer.process_spectrum_store_modifications(self.spectra[spectrum_id])
             self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[spectrum_id])
-
-
 
 

library_spectra_validation/tests/test_library_handler.py

@@ -61,3 +61,10 @@ def test_user_metadata_change():
     spectrum_id = 0
     library_handler.user_metadata_change(spectrum_id=spectrum_id, field_name="smiles", user_input="CCC")
     assert library_handler.spectra[spectrum_id].get("smiles") == "CCC"
+
+def test_return_():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    modifications, failed_requirements, metadata = library_handler.return_user_validation_info(spectrum_id=spectrum_id)
+    # todo add checks that tests that the expected output is given.
+    print(metadata)

library_spectra_validation/validation_pipeline.py

@@ -15,6 +15,9 @@
 
 logger = logging.getLogger("matchms")
 
+METADATA_FIELDS_OF_INTEREST = ["parent_mass", "precursor_mz", "adduct", "smiles",
+                                "compound_name", "inchi", "inchikey", "charge", "ionmode"]
+
 
 class Modification:
     def __init__(self, metadata_field, before, after, logging_message, validated_by_user):
@@ -34,9 +37,7 @@ def __init__(self, metadata_field, logging_message):
 def find_modifications(spectrum_old, spectrum_new, logging_message: str):
     """Checks which modifications have been made in a filter step"""
     modifications = []
-    metadata_fields_to_check = ["parent_mass", "precursor_mz", "adduct", "smiles",
-                                "compound_name", "inchi", "inchikey", "charge", "ionmode"]
-    for metadata_field in metadata_fields_to_check:
+    for metadata_field in METADATA_FIELDS_OF_INTEREST:
         if spectrum_old.get(metadata_field) != spectrum_new.get(metadata_field):
             modifications.append(
                 Modification(metadata_field=metadata_field,